Integration of miRNA-mRNA co-expression network reveals potential regulation of miRNAs in hypothalamus from sterile triploid crucian carp

The sterile triploid crucian carp (TC) has growth superiority which is generated from crossing between diploid red crucian carp (Carassius carassius red var. ♀) (RC) and tetraploid hybrid linage [derived from RC (♀) × common carp (Cyprinus carpio, ♂) (CC)]. Hypothalamus is an important control center for hormone releasing participating in gonadal development. In the present study, the microRNA (miRNA) alternations in the hypothalamus from RC, CC and TC were analyzed. A total of 143 known miRNAs and 519 novel miRNAs were identified from the hypothalamus. Thereinto, miR-7a, miR-128 and miR-9-3p were the most abundant miRNAs accounting for 13.37%, 12.01% and 11.15% of all the miRNA reads, respectively. A total of 109, 208 and 228 differentially expressed miRNAs (DEMs) were identified from RC vs TC, CC vs TC and CC vs RC, respectively. For these DEMs, 46 miRNA-mRNA pairs were identified by miRNA target prediction. In addition, using weighted gene co-expression network analysis (WGCNA), 17 modules of co-expressed miRNAs and mRNA were constructed and yellow module had the highest correlation with the sterile triploid. A total of 107 novel miRNAs, 29 conserved miRNAs and 1343 genes were contained in yellow module and metabolic processes, biosynthetic processes, chromosome organization, cytoskeleton organization, gene expression and axis specification were enriched GO terms in this module. The top three hub miRNAs were let-7a, miR-100 and miR-122 which were correlated with 1086, 1172 and 1222 genes, respectively. These results indicated that the hub miRNAs and their regulated gene network play a central role in controlling endocrine secretion and gamete maturation. In addition, the abnormal expression of these miRNAs contributes to the sterility of TC. The present evidence provides insights into the miRNA and gene constructed network of sterility in triploid fish.